A bacterial strain SY-97 that showed algicidal activity against Cochlodinium polykrikoides was isolated from coastal water of Uljin (eastern coast of Korea) in August, 2005. The isolated strain was identified as Brachybacterium sp. by morphological and biological tests, and analysis of 16S rDNA sequence. The optimal culture conditions for the growth of strain SY-97 were 30℃, initial pH 7.0, and salinity 2.0%. From the result of cell culture insert experiment, Brachybacterium sp. SY-97 is assumed to produce secondary metabolites which have algicidal activity. When 10% culture filtrate of this strain was applied to C. polykrikoides (1.2 × 104 cells/㎖) cultures, 100% of C. polykrikoides cells was destroyed within 15 hours. The released algicides were heat-tolerant to 100℃ and stable in pH 6.0～10.0. These results suggest that Brachybacterium sp. SY-97 is potentially useful for controlling outbreaks of C. polykrikoides.